Strain identifier

BacDive ID: 6014

Type strain: Yes

Species: Halomonas halodenitrificans

Strain history: CIP <- 1998, NCIMB <- M. Ingram <- N.E. Gibbons, Micrococcus halodenitrificans

NCBI tax ID(s): 1121941 (strain), 28252 (species)

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General

@ref: 379

BacDive-ID: 6014

DSM-Number: 735

keywords: genome sequence, 16S sequence, Bacteria, Gram-negative

description: Halomonas halodenitrificans DSM 735 is a Gram-negative bacterium that was isolated from wiltshire bacon curing brine.

NCBI tax id

NCBI tax idMatching level
28252species
1121941strain

strain history

@refhistory
379<- CCM <- N.E. Gibbons (Micrococcus halodenitrificans)
119801CIP <- 1998, NCIMB <- M. Ingram <- N.E. Gibbons, Micrococcus halodenitrificans

doi: 10.13145/bacdive6014.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Oceanospirillales
  • family: Halomonadaceae
  • genus: Halomonas
  • species: Halomonas halodenitrificans
  • full scientific name: Halomonas halodenitrificans (Robinson and Gibbons 1952) Dobson and Franzmann 1996

  • synonyms

    @refsynonym
    20215Paracoccus halodenitrificans
    20215Micrococcus halodenitrificans

@ref: 379

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Oceanospirillales

family: Halomonadaceae

genus: Halomonas

species: Halomonas halodenitrificans

full scientific name: Halomonas halodenitrificans (Robinson and Gibbons 1952) Dobson and Franzmann 1996

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
119801negativeoval-shapedno
69480negative99.5

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
379MEDIUM 514 PLUS ADDITIONAL SALT (DSMZ Medium 514b)yeshttps://mediadive.dsmz.de/medium/514bName: MEDIUM 514 plus additional salt (DSMZ Medium 514b) Composition: NaCl 19.45 g/l Agar 17.5 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
39298MEDIUM 192 - for Alteromonas rubrayesDistilled water make up to (250.000 ml);Agar (15.000 g);Yeast extract (3.000 g);Peptone (5.000 g);Synthetic sea solution - M0216 (750.000 ml)
119801CIP Medium 192yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=192

culture temp

@refgrowthtypetemperature
379positivegrowth28
39298positivegrowth25
119801positivegrowth15-30
119801nogrowth5
119801nogrowth37
119801nogrowth41
119801nogrowth45

Physiology and metabolism

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 90.246

halophily

@refsaltgrowthtested relationconcentration
119801NaClpositivegrowth2-10 %
119801NaClnogrowth0 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1198014853esculin-hydrolysis
119801606565hippurate-hydrolysis
11980117632nitrate-builds gas from
11980117632nitrate+reduction
11980116301nitrite-builds gas from
11980116301nitrite-reduction
11980115792malonate-assimilation
11980117234glucose-degradation

metabolite production

  • @ref: 119801
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11980115688acetoin-
11980117234glucose-

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase-3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)-
68382esterase (C 4)+
68382alkaline phosphatase-3.1.3.1
119801oxidase-
119801beta-galactosidase-3.2.1.23
119801alcohol dehydrogenase-1.1.1.1
119801gelatinase-
119801amylase-
119801caseinase-3.4.21.50
119801catalase-1.11.1.6
119801tween esterase-
119801gamma-glutamyltransferase+2.3.2.2
119801lecithinase-
119801lipase-
119801lysine decarboxylase-4.1.1.18
119801ornithine decarboxylase-4.1.1.17
119801phenylalanine ammonia-lyase-4.3.1.24
119801tryptophan deaminase-
119801urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
119801--+--+-----+---+----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119801---------------------------------------------------------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
379wiltshire bacon curing brineCanadaCANNorth America
119801Bacon curing brineUnited KingdomGBREuropeWiltshire

isolation source categories

Cat1Cat2Cat3
#Engineered#Food production#Meat
#Condition#Saline

taxonmaps

  • @ref: 69479
  • File name: preview.99_91581.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_48;96_37848;97_48132;98_63115;99_91581&stattab=map
  • Last taxonomy: Halomonas
  • 16S sequence: L04942
  • Sequence Identity:
  • Total samples: 46
  • soil counts: 8
  • aquatic counts: 19
  • animal counts: 12
  • plant counts: 7

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
3791Risk group (German classification)
1198011Risk group (French classification)

Sequence information

16S sequences

  • @ref: 379
  • description: Paracoccus halodenitrificans 16S ribosomal RNA sequence
  • accession: L04942
  • length: 1531
  • database: nuccore
  • NCBI tax ID: 28252

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Halomonas halodenitrificans DSM 735GCA_000620045scaffoldncbi1121941
66792Halomonas halodenitrificans DSM 7351121941.3wgspatric1121941
66792Halomonas halodenitrificans DSM 7352556921012draftimg1121941

GC content

  • @ref: 379
  • GC-content: 65.0

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69480gram-positivegram-positivePositive reaction to Gram-stainingno99.5no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no96.813no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes79.085no
69480spore-formingspore-formingAbility to form endo- or exosporesno90.246no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno97.598no
69480flagellatedmotile2+Ability to perform flagellated movementno68.703no

External links

@ref: 379

culture collection no.: DSM 735, ATCC 13511, CCM 286, NCMB 700, CIP 105456, IAM 13950, IFO 14912, NCIMB 700, CECT 5012

straininfo link

  • @ref: 75500
  • straininfo: 35825

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Metabolism12615395Thermokinetic description of anaerobic growth of Halomonas halodenitrificans using a static microcalorimetric ampoule technique.Maskow T, Babel WJ Biotechnol10.1016/s0168-1656(02)00341-32003Anaerobiosis, Calorimetry/instrumentation/*methods, Computer Simulation, Glycerol/metabolism, Halomonas/*growth & development, *Models, Biological, Nitrates/metabolism, Reproducibility of Results, Sensitivity and Specificity, Statistics as Topic
Metabolism16309773Chip calorimetry for the monitoring of whole cell biotransformation.Maskow T, Lerchner J, Peitzsch M, Harms H, Wolf GJ Biotechnol10.1016/j.jbiotec.2005.10.0082005Anaerobiosis, *Biotransformation, Calorimetry/instrumentation/*methods, Cells, Cultured, Escherichia coli/growth & development/metabolism, Halomonas/growth & development/metabolism, Hot Temperature, Kinetics, Models, Biological, Thermodynamics, Time FactorsStress
Phylogeny33351740Halomonas icarae sp. nov., a moderately halophilic bacterium isolated from beach soil in India.Pandiyan K, Kushwaha P, Bagul SY, Chakdar H, Madhaiyan M, Krishnamurthi S, Kumar P, Karthikeyan N, Singh A, Kumar M, Singh UB, Saxena AKInt J Syst Evol Microbiol10.1099/ijsem.0.0046112020Bacterial Typing Techniques, Base Composition, Bathing Beaches, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Halomonas/*classification/isolation & purification, India, Nucleic Acid Hybridization, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitle
379Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 735)https://www.dsmz.de/collection/catalogue/details/culture/DSM-735
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
39298Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17477
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
68382Automatically annotated from API zym
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
75500Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID35825.1StrainInfo: A central database for resolving microbial strain identifiers
119801Curators of the CIPCollection of Institut Pasteur (CIP 105456)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105456